7BQI | pdb_00007bqi

Crystal structure of FYCO1 RUN domain

• PDB DOI: https://doi.org/10.2210/pdb7BQI/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-24 Released: 2020-08-05 
• Deposition Author(s): Sakurai, S., Shimizu, T., Ohto, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.240 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.

Sakurai, S., Shimizu, T., Ohto, U.

(2020) Acta Crystallogr F Struct Biol Commun 76: 326-333

• PubMed: 32744243 
• DOI: https://doi.org/10.1107/S2053230X20009012
• Primary Citation Related Structures: 
  7BQI


• PubMed Abstract: 
  

  FYCO1 is a multidomain adaptor protein that plays an important role in autophagy by mediating the kinesin-dependent microtubule plus-end-directed transport of autophagosomes. FYCO1 contains a RUN domain, which is hypothesized to function as a specific effector for members of the Ras superfamily of small GTPases, but its role has not been well characterized and its interaction partner(s) have not been identified. Here, the crystal structure of the FYCO1 RUN domain was determined at 1.3 Å resolution. The overall structure of the FYCO1 RUN domain was similar to those of previously reported RUN domains. Detailed structural comparisons with other RUN domains and docking studies suggested a possible interaction interface of the FYCO1 RUN domain with small GTPases of the Ras superfamily.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.87 kDa 
• Atom Count: 1,603 
• Modeled Residue Count: 174 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FYVE and coiled-coil domain-containing protein 1	A	183	Homo sapiens	Mutation(s): 0  Gene Names: FYCO1, ZFYVE7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQS8 (Homo sapiens) Explore Q9BQS8  Go to UniProtKB:  Q9BQS8
PHAROS:  Q9BQS8 GTEx:  ENSG00000163820

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.119	α = 90
b = 48.119	β = 90
c = 142.671	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Sakurai, S., Shimizu, T., Ohto, U.

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description